Background: The Ph chromosome is the most frequent karyotypic aberration in adults with ALL and it represents the single most significant adverse prognostic marker. Despite the encouraging results achieved with imatinib, resistance develops rapidly and is quickly followed by disease progression. Recently, the introduction of array-based analysis of single nucleotide polymorphism (SNP) has allowed the rapid determination of genome-wide allelic information at high density for a DNA sample. Patients and Methods: In order to identify, at submicroscopic level, genetic lesions which can escape standard cytogenetic observations and may contribute to leukemogenesis and resistance, we profiled, until now, the genomes of 18 patients out of 55 Ph+ ALL patients treated in our institute with imatinib or dasatinib. 250 ng of genomic DNA were processed on 500K SNP array according to protocols provided by the manufacturer (Affymetrix Inc., Santa Clara, CA, USA). Copy number state was calculated with respect to a set of 48 Hapmap normal individuals and a diploid reference set of samples obtained from acute leukaemia cases in remission using Partek® Genomics Suite. Fluorescence in situ hybridization (FISH) and real-time quantitative PCR were performed to validate our results. Results: We identified multiple copy number alterations per case, with deletions outnumbering amplification almost 3:1. Lesions varied from loss or gain of complete chromosome arms (trisomy 4, monosomy 7, loss of 9p, 10q, 14q, 16q and gain of 1q and 17q) to microdeletions and microduplications targeting genomic intervals. The common microdeletions included 1p36.21 (PRAMEF), 3q29 (TFCR), 8p23 (DEFB105A), 14q11.2 (DAD1), 16p13.11 (PDXDC1, NTAN1, RRN3), 16p11.2 (SPN) and 19p13.2 (CARM1, SMARCA4). Some genomic alterations were identified in genes regulating B-lymphocyte differentiation, such as PAX5 (n=3), BLNK (n=1) and VPREB1 (n=6), IKZF1 (n=7) and in genes with an established role in leukemogenesis, such as MDS, BTG1, MLLT3, RUNX1. The most frequently affected genes were those controlling G1/S cell cycle transition (e.g. CDKN2A and CDKN2B). Furthermore, many of the deletions detected included genes encoded for phosphatase proteins (e.g. PTPRD, PPP1R9B, PTPN18) and for zinc-finger proteins. It is noteworthy that some lesions felt in regions lacking annotated genes. Discussion: Using high-resolution genome wide approach we showed that multiple sub-microscopic genomic anomalies, which may be suspected to contribute to leukemogenesis and used as targets for existing or novel drugs, frequently occur in Ph+ ALL
High-resolution genomic profiling of Philadelphia chromosome-positive (Ph+) acute lymphoblastic leukemia (ALL) patients identified novel recurrent copy number variations involved in both pathogenesis and resistance to tyrosine kinase inhibitors
Iacobucci, Ilaria;LONETTI, ANNALISA;Testoni, Nicoletta;Soverini, Simona;Papayannidis, Cristina;PESSION, ANDREA;
2008
Abstract
Background: The Ph chromosome is the most frequent karyotypic aberration in adults with ALL and it represents the single most significant adverse prognostic marker. Despite the encouraging results achieved with imatinib, resistance develops rapidly and is quickly followed by disease progression. Recently, the introduction of array-based analysis of single nucleotide polymorphism (SNP) has allowed the rapid determination of genome-wide allelic information at high density for a DNA sample. Patients and Methods: In order to identify, at submicroscopic level, genetic lesions which can escape standard cytogenetic observations and may contribute to leukemogenesis and resistance, we profiled, until now, the genomes of 18 patients out of 55 Ph+ ALL patients treated in our institute with imatinib or dasatinib. 250 ng of genomic DNA were processed on 500K SNP array according to protocols provided by the manufacturer (Affymetrix Inc., Santa Clara, CA, USA). Copy number state was calculated with respect to a set of 48 Hapmap normal individuals and a diploid reference set of samples obtained from acute leukaemia cases in remission using Partek® Genomics Suite. Fluorescence in situ hybridization (FISH) and real-time quantitative PCR were performed to validate our results. Results: We identified multiple copy number alterations per case, with deletions outnumbering amplification almost 3:1. Lesions varied from loss or gain of complete chromosome arms (trisomy 4, monosomy 7, loss of 9p, 10q, 14q, 16q and gain of 1q and 17q) to microdeletions and microduplications targeting genomic intervals. The common microdeletions included 1p36.21 (PRAMEF), 3q29 (TFCR), 8p23 (DEFB105A), 14q11.2 (DAD1), 16p13.11 (PDXDC1, NTAN1, RRN3), 16p11.2 (SPN) and 19p13.2 (CARM1, SMARCA4). Some genomic alterations were identified in genes regulating B-lymphocyte differentiation, such as PAX5 (n=3), BLNK (n=1) and VPREB1 (n=6), IKZF1 (n=7) and in genes with an established role in leukemogenesis, such as MDS, BTG1, MLLT3, RUNX1. The most frequently affected genes were those controlling G1/S cell cycle transition (e.g. CDKN2A and CDKN2B). Furthermore, many of the deletions detected included genes encoded for phosphatase proteins (e.g. PTPRD, PPP1R9B, PTPN18) and for zinc-finger proteins. It is noteworthy that some lesions felt in regions lacking annotated genes. Discussion: Using high-resolution genome wide approach we showed that multiple sub-microscopic genomic anomalies, which may be suspected to contribute to leukemogenesis and used as targets for existing or novel drugs, frequently occur in Ph+ ALLI documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
